1. Field of the Invention
The present invention relates to a new representation method of RNA pseudoknot structures and a visualization method of the RNA pseudoknot structures and a whole RNA structure containing the pseudoknots, and more particularly to a visualization method of RNA pseudoknot structures for the prediction and modeling thereof.
2. Description of the Related Art
A pseudoknot structure in a RNA molecule is a tertiary structural element formed when bases in a loop of secondary structure pair with complementary bases outside the loop. RNA pseudoknots are not only an essential structural element to form tertiary structures of RNA, but also are responsible for important functions of RNA.
Although several computer programs for visualizing a secondary structure of RNA are available (for example, those disclosed by De Rijk & De Wachter, 1997 and Han et al., 1999), there are no automated techniques or programs for visualizing a RNA pseudoknot structure. In the sense of graph theory, a drawing of RNA secondary structure is a tree, whereas a drawing of RNA pseudoknot structure is a graph. Thus, drawing RNA pseudoknot structures requires many more computations to visualize, compared to RNA secondary structures.
Currently, RNA pseudoknots are represented by drawing RNA secondary structures first, using a visualizing program of RNA secondary structures, and then either adding line segments to the secondary structure drawings or modifying the RNA secondary structure drawings with the aid of a graph-editing function. Such a drawing relying on a significant amount of manual work for visualization is difficult and yields an unsatisfactory result, as a whole RNA size increases.
FIGS. 1a to 1d display conventional representations of H-type pseudoknots of RNA (Hilbers et al., 1998). FIG. 1a is a general configuration for representing a pseudoknot structure in which dotted lines indicate base pairings between bases in a hairpin loop and bases in the 3′ direction of the RNA sequence. FIGS. 1b to 1d represent pseudoknot structures obtained by eliminating one of three loops from the pseudoknot structure of FIG. 1a, and by stacking stem 1 and stem 2 coaxially, thereby mimicking a single stem in the representation. In particular, FIGS. 1b to 1d can be obtained from FIG. 1(a) by eliminating loop 1, loop 2 and loop 3, respectively. The pseudoknot structure of FIG. 1(c) is the most abundant among natural RNAs.
However, the conventional method for the representation of pseudoknots has a disadvantage in that there are many edge crossings in the representation, thus being difficult to follow RNA sequences from a 5′-end to a 3′-end, so making it hard to easily recognize the pseudoknot structures.